PLoS ONE – a personal farewell

This is my last day as the Publisher of PLoS ONE, and I wanted to mark it with a brief blog post.

When I came to work on PLoS ONE (in March 2008), the journal was in its infancy, but was clearly going places.  At that time it was receiving about 280 submissions, and publishing about 170 articles, per month. The journal is now receiving over 3,100 submissions per month and in May it should exceed 2,000 publications for the first time ever. PLoS ONE now publishes more articles per month than all but about 20 journals worldwide publish in a year, and in 2012 it could publish almost 3% of the STM literature.

But although the publication volume of the journal has made it very visible, it is how it got there which is the truly interesting story. PLoS ONE was a radical concept when proposed by the PLoS Founders – a journal which would judge submissions only on scientific and methodological soundness, leaving any subjective determinations of impact, scope, or relevance to the post-publication phase. As a result, many commentators felt that it could become a dumping ground for otherwise unpublishable work, or would in some way be a vanity press. But this was never the case. In fact, PLoS ONE has applied exemplary standards to its publication practices; it has rigorously enforced global and local ethical standards; it has treated all authors with courtesy and respect; and it has peer reviewed all submitted content to the highest levels – collectively, these are things which have shown that the journal is serious about the ways in which it will evaluate and handle submitted articles. Today, more than 75% of authors who publish in PLoS ONE have selected the journal as their first or second choice publication venue, and the citation activity of published articles is incredibly high (for example, for those articles which are 12 months or older, 88% have 1 or more citations, and 66% have 3 or more). In addition, the journal has won two awards for Innovation from Industry and Community bodies.

Clearly this radical approach to the evaluation and publication of scientific results has been extremely well received. As a result it is my belief that PLoS ONE has caused (and will continue to cause) a seismic shift in the scholarly publication landscape. It represents a real force for positive change in the way in which academic articles are evaluated and distributed.

Therefore, it is with a sense of considerable sadness that today is my last day on the Journal – running PLoS ONE has been the high point of my career. I would like to take this opportunity to thank everyone who has worked on the journal over the years – without the efforts of the Academic Editors (who now number more than 3,000), the Peer Reviewers (who number almost 75,000) and the staff (located in both our offices, and in various partner organizations) PLoS ONE would not have been the success it is. The journal is, of course, in safe hands – we have a strong organization of experienced staff, and dedicated Academic Editors who, I know, will take the journal to new heights in the coming years.

Thank you,

Peter Binfield,

Publisher PLoS ONE

.

Category: General | Tagged | 3 Comments

New PLoS ONE Manuscript Submission and Peer Review System is Live

At 10 am (PST) on Monday 26th July, PLoS ONE  moved to a new software system for our manuscript submission and peer review process —Editorial Manager® from Aries Systems (referred to as “PLoS EM”). The other PLoS titles will migrate to the new platform later this summer.

If you are a PLoS ONE author (or reviewer) who had a manuscript ‘in process’ with us before this date then your manuscript will continue to be processed in the ‘old’ system for a period of time before it is transferred to the ‘new’ system. You will receive clear notification as to where you should log in to find your manuscript, and more information about this process can be found at our explanatory website.

This new system will make it easier to track the progress of your manuscript and will provide other important user benefits such as:

•    Reliable system performance
•    Easier figure submission—one zipped file upload
•    Fast PDF preview upon submission
•    Multi-tier subject taxonomy
•    Your own home page to track the progress of your manuscript

Category: Manuscript submission and peer review system, Peer review, Service improvements | Tagged , | 1 Comment

PLoS ONE: Editors, contents and goals

This post cross posted from the PLoS.org blog

Recently, Kent Anderson posted some misleading comments about PLoS ONE on the Scholarly Kitchen, a blog site established by the Society for Scholarly Publishing. Although several PLoS community supporters have responded swiftly and vigorously to the comments, PLoS has also decided to make a public statement because Mr Anderson’s comments were extreme and have caused bad feeling particularly among the editorial board members who work so hard to make PLoS ONE a success (on a voluntary basis).

Mr Anderson’s posting and his subsequent responses to comments misrepresent PLoS ONE in four main areas: the PLoS ONE editorial board, the editorial process; the content being published; and the overall goal of PLoS ONE.

1. The editorial board

During his post, Mr Anderson implied that the PLoS ONE Editorial Board (who are now 1,000 strong and as academic editors are responsible for the editorial decisions on PLoS ONE) are accepting sub-standard papers simply to make more money for PLoS. Several academic editors took justified exception to this in the comment thread and elsewhere. The tremendous success of PLoS ONE is in large part a result of the dedication and commitment of the PLoS ONE Editorial Board, and any implication that the PLoS ONE Board members are collectively doing a poor job of evaluating submissions is unjustified.

2. The editorial process

The PLoS ONE editorial and peer review process is very similar to the editorial process on any journal, and is clearly explained on the PLoS ONE web site. The critical difference, and the thing that makes PLoS ONE potentially revolutionary, is that the editors and peer reviewers make no judgment as to the potential impact of the work. Their goal is to focus on scientific rigour alone, although this is by no means an easy task.

Every submission goes through a very substantial quality control check before it reaches an academic editor. This check covers reporting standards, research ethics, competing interests, funding information and so on. We believe that our ‘QC check’ is one of the most extensive and rigorous processes in the industry, and it is overseen by professional editors who are frequently consulted in advance of further peer review. Submissions are then assigned to academic editors, who send the articles to external peer reviewers and take overall responsibility for the editorial decision on the submission assigned to them. Submissions are assessed specifically against the PLoS ONE editorial criteria. We also provide summary statistics on the peer review process and as repeatedly evidenced by published PLoS ONE authors, submissions typically receive excellent peer review comments and go through multiple revisions before ultimately being accepted. PLoS and the Academic Editors are committed to achieving very high standards in the editorial process.

3. The content

Mr Anderson’s post seems to be prompted by some concerns about a specific recent PLoS ONE article, which was critiqued by one of his co-editors on the Scholarly Kitchen blog. The irony here is that one of the goals of PLoS ONE is to open up this kind of dialogue post-publication, so that everyone can benefit from a more open discussion. What we are striving to do better is to capture more of this discussion and link it to the articles themselves.

Putting that one article aside, the implication of the post is that PLoS ONE content is substandard in some way, but evidence to support this claim is not provided. In fact, we do have evidence from usage, citation and media/blog coverage that the quality of content in PLoS ONE is extremely high, and would compare favourably with most journals. For example over 84% of the more than 2700 articles published in 2008 have been cited (from Scopus data), and 39% cited 4 times or more. These and other article-level metric data are publicly available (for all PLoS Journals) on our web site.

PLoS ONE has also been selected for coverage by all major indexing services, including Web of Science and Medline. A round-up of some of the most high-profile content published in PLoS ONE in 2009 was posted in January.

4. The goal of PLoS ONE

As mentioned above, the key innovation of PLoS ONE is that the peer review process involves no judgment about the potential impact of a submission. This is because our view is that the current system of sorting the almost 2 million articles that are published each year, into the existing set of 25,000 journals before publication, with all the delays and redundancy that this involves, is not the best way to organize all research findings in an online world.

Instead, PLoS ONE peer reviews submissions on the basis of scientific rigour, leaving the assessment of the value or significance of any particular article to the post-publication phase. We would fully agree that it is in the post-publication phase that PLoS has not yet achieved as much as we would like. Nevertheless, the addition of article-level metrics to all PLoS content last year is an important step in this direction and there will be further developments in this area.

PLoS ONE thus frees authors from a system of journals that is biased against publication, which means that authors can publish their work swiftly. We have been surprised and delighted that so many authors (now well over 60,000 of them) have supported PLoS ONE by sending us their submissions. As a result of this groundswell of support from the research community, the growth of PLoS ONE has been spectacular and, we believe, unparalleled in the history of scientific publishing (the journal is less than 4 years old and is on target to be the largest peer-reviewed journal in the world this year).

Given that the costs of publication are fully covered by publication fees, it is true that PLoS ONE has helped to move PLoS much closer towards independent economic sustainability. However, it is also the case that the PLoS Community Journals (PLoS Computational Biology, PLoS Pathogens  and PLoS Genetics) launched in 2005 are fully economically sustainable through publication fees and are now making a positive financial contribution to our organisation. There is no question that the financial impact of PLoS ONE is important for PLoS and for open-access publishing more broadly, but to focus purely on this aspect of PLoS ONE is to miss the real significance of PLoS ONE, which was established as an innovative publication vehicle aiming to dramatically improve the pace and efficiency of scientific communication relative to the established order of academic journals.

This significance was formally recognized last year, when PLoS ONE received a major industry award from ALPSP for publishing innovation. The judges indicated that PLoS ONE “combines the traditional values of the journal with innovative online features to create an inclusive and efficient publication channel. It is bold and successful and shaping the future of publishing.”

Finally, we must acknowledge the tremendous support of the research community who as authors, reviewers and editors have already established PLoS ONE as an efficient and effective peer-reviewed publication, which is successfully challenging the traditional notion of a journal.

Pete Binfield, Publisher (PLoS ONE and PLoS Community Journals)
Mark Patterson, Director of Publishing, PLoS

Category: General, Peer review | Tagged , | 2 Comments

Update to PLoS Article-Level Metrics Data

As you may be aware, as part of our ongoing article-level metrics program, we provide a downloadable Excel file for the entire dataset (3 Mb zipped, but 35 Mb when unzipped). The first such file was created when we launched the usage data (in September 2009) and we have just updated it with the latest data (with data correct up to January 31st 2010). Going forwards, we plan to update this spreadsheet every other month, starting in April.

The main changes with this latest version (other than containing a more recent dataset) are:

  • The addition of the ‘missing’ usage data for all our articles.
    • We now have a complete usage dataset for all articles, going back to day of publication (previously some articles missed the usage data for their early years)
  • The addition of data from researchblogging.org. Researchblogging.org are a blog aggregating service and we now include their data as part of the article-level metrics data set (as described in an earlier post)
  • An update to the various  journal level summary tables

Some people have already started analysing our data and we encourage anyone who is interested to take this dataset and do their own analysis. Also be aware that the ‘live’ data for each article can be accessed by clicking on the link: “Download raw Metrics data as XML” which can be found at the bottom of each article’s Metrics tab.

Category: article-level metrics | Tagged | 3 Comments

Science Commons presentation on PLoS ONE and Article-Level Metrics

On Feb 20th, Microsoft hosted a “Science Commons Symposium” at their HQ in Redmond, WA. It was a great line up of speakers, and I was honored to be among them with an invitation to talk about PLoS ONE and our article-level metrics program.

Several people blogged about the meeting, and Brian Glanz provided an excellent running commentary for the entire day.

Courtesy of Microsoft Research, the full video coverage of all the talks are now online as follows: Session 1 (Microsoft Research; Cameron Neylon; Jean-Claude Bradley); Session 2 (Antony Williams; Peter Murray-Rust); Session 3 (Heather Joseph; Stephen Friend); and Session 4 (starring myself, in a warm up role for the keynote by John Wilbanks).You will need to install Silverlight to view the videos.

This was an excellent meeting, for which Microsoft and Science Commons deserve a lot of praise – I recommend the video coverage for anyone who couldnt be there.

Category: article-level metrics, Presentations | Tagged , | Leave a comment

New Enhanced Articles published in the SGC Collection

Late last year we launched a new Collection of articles (titled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC”) which makes use of leading edge, three dimensional molecular animation technology and today we have added 2 new articles to this Collection (which will continue to grow over time).

The new articles are:

” Crystal Structures of the ATPase Domains of Four Human Hsp70 Isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B’, and HSPA5/BiP/GRP78″ by Wisniewska M, Karlberg T, Lehtiö L, Johansson I, Kotenyova T, et al.

and

“Structural Biology of Human H3K9 Methyltransferases” by Wu H, Min J, Lunin VV, Antoshenko T, Dombrovski L, et al.

and in each case, the enhanced version (which provides seamless integration of interactive 3D structures into the actual text of the article)  may be accessed by clicking on the links in the abstract.

Category: Collections, Functionality | Tagged , | Leave a comment

PLoS ONE indexed by Web of Science

Reposted from a post made by Mark Patterson to the PLoS Blog.

Today we learned that by the end of this week PLoS ONE (in keeping with all other PLoS journals) will be indexed by the Web of Science – this is an important literature discovery tool that many people use and so we are pleased to be indexed. PLoS ONE is also indexed by a host of other services such as PubMed, MEDLINE, PubMed Central, Scopus, Google Scholar, the Chemical Abstracts Service (CAS), EMBASE, AGRICOLA, PsycINFO, Zoological Records, FSTA (Food Science and Technology Abstracts), GeoRef, and RefAware.

Initially, coverage in the Web of Science will include new PLoS ONE articles plus those published in 2008 and 2009, and will be expanded to the articles published in 2006 (when PLoS ONE was launched) and 2007 in the coming weeks. Inclusion in the Web of Science also means that in June 2010 PLoS ONE will receive journal-level citation data from Thomson Reuters including a 2- and 5-year Impact Factor and Eigenfactor metrics.

As we have previously indicated, PLoS believes that research articles are best assessed on their own merits, rather than on the basis of the journal (and its impact factor) where the work happens to be published. While we are happy that PLoS ONE articles will become more discoverable as a result of their inclusion in the Web of Science, we will continue to push forward with our Article-Level Metrics program.

Naturally, we understand that inclusion in the Web of Science is significant for many academics whose research output is still measured by traditional means. We hope that this news encourages even more scientists to publish their work in PLoS journals, to benefit from the article-level metrics that are provided for every PLoS article (for example, this PLoS ONE article), and to ensure that all interested users have open access to their research.

Category: article-level metrics | Tagged | Leave a comment

PLoS ONE Review of 2009

It was on Dec 20th, 2006 that PLoS ONE launched, and 2009 (only our third full year of publication) has been packed full of exciting developments.  To note our birthday, I took the opportunity to round up the major events of the past 12 months. There have been an awful lot of them and it is a tribute to our staff and academic editors that we were able to achieve all of the following while increasing our publication volume from 2,726 articles published in 2008 to 4,400 expected in 2009 (something which, we believe, now makes us the third largest journal in the world, by publication volume).

The start of the year saw us developing new functionality, with the launch of Collections on PLoS ONE. This began with the publication of the ‘Stress-Induced Depression and Comorbidities’ Collection in January, followed by our second in February – the  PLoS ONE Paleontology Collection. We subsequently launched the Prokaryotic Genome Collection in June and the Structural Genomics Consortium Collection in October (a collection which provides ‘enhanced versions’ of papers, incorporating advanced 3D interactive simulation software – an excellent example of the creative re-use of Open Access content).

In March, we launched everyONE, our community blog site; we announced our ability to accept LaTeX submissions; and we upgraded our site with a redesigned ‘tabbed’ user interface to accommodate our newly launched Article-Level Metrics functionality (of which more later).

In April, we announced our ‘Blog Post of the Month Competition’ (in collaboration with researchblogging.org) which has since gone on to award a winner every month.

In May, we redesigned our email Table of Contents alerts so that recipients now receive an email categorized by subject area, and this was also the month in which we publicly thanked the 9,000 peer reviewers who gave us their expert opinions during 2008.

Our 2009 media coverage will be reviewed by Bex in a different post, but in May we published a paper that sparked our largest media story of the year – the Darwinius masillae (or ‘Ida’) paper – “Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology”. The coverage of this paper was overviewed in three separate blog posts.  

May also saw a major event in the development of PLoS’s technology platform – with the migration of PLoS Biology and PLoS Medicine, we were finally able to have all seven of our titles on Topaz, which is now our shared online platform.

In July, we began a partnership with DeepDyve to improve our search capabilities and we also launched the “Worth a Thousand Words” blog series (featuring a selected image from each week’s publications). July also saw PLoS publicly express our opinion that there is more value in measuring impact at the article level than at the journal level – something which coincided with the announcement that we would no longer be promoting Impact Factors on our sites.

In August, PLoS ONE was featured in the popular internet comic, “PhD Comics” as part of their “Nature vs Science” series, and in the same month PLoS launched an important experiment in rapid publication – PLoS Currents: Influenza, a collaboration between PLoS, Google Knol and the NCBI

In September, PLoS ONE was immensely proud to win the ALPSP Award for Publishing Innovation, 2009 – this is a major industry award and a testament to the rapid pace of innovation that the journal has pioneered in the 3 years since launch.

September was also the month that saw our Article-Level Metrics program expand in a significant way, by displaying usage data on every article in the PLoS corpus. In December, we also added data from ResearchBlogging.org to the program.  We regard Article-Level Metrics as a significant new development in academic publishing and we  expect to significantly expand it in 2010. Several presentations were made through the year on the topic of Article-level Metrics, for example to NISO, to the ElPub Conference, and to UCSF/Berkeley and these are all archived with audio if you wanted to delve into the details.

In October, OASPA, the new association for Open Access Scholarly Publishers was launched and PLoS was proud to be a founding member. This coincided with Open Access Week, 2009. And in November, in response to many requests over the years, we launched our new PLoS store.

And finally, after a year of incredible developments, 2009 has culminated with what may yet turn out to be the most significant development of all – the request by the White House Office of Science and Technology Policy (OSTP) for public comments on the issue of broadening public access to publicly funded research. You still have time to provide your feedback and there would be no better New Year resolution than to make your voice heard in this forum.

Thank you to everyone who has supported us in 2009, and over the last three years – in particular thank you to our (almost) 1,000 Academic Editors, all of our peer reviewers and of course, all of our authors. We look forward to publishing more great science in 2010!

Category: Ask EveryONE, Functionality | Tagged , | 1 Comment

Article Level Metrics presentation to Berkeley and UCSF

A few weeks ago I had the chance to present the PLoS Article Level Metrics program to audiences at both Berkeley and UCSF (via a simulcast). The organisers allowed me to devote a full hour to our program, and as a result this is the most detailed presentation that we have made on ALMs to date.

The presentation was recorded and so, by the power of multi-multi media, it is now available in many different formats – as a webcast (with both audio and video versions), as a YouTube video, and as a slidecast at MyPlick (incorporating audio, synced with the slides).

In addition, readers may be interested to learn that a FriendFeed room now exists for Article Level Metrics. We do not regard Article Level Metrics as a PLoS-only project and we hope (and expect) that other publishers will adopt the concepts that we are pioneering. Therefore, if was gratifying that this discussion forum was created by members of the community outside of PLoS.  It is being used as a place to collect and discuss issues of relevance to the concept of Article Level Metrics (i.e. it is not specific to PLoS)  and it is definitely worth subscribing to.

Category: article-level metrics, Presentations | Tagged , | 2 Comments

Interactive 3D Molecules in PLoS ONE articles

Today PLoS ONE launched a new Collection titled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” which makes use of leading edge, three dimensional molecular animation technology.

SGC Collection LogoBecause of our Open Access license, which allows anyone to re-use our content provided they make appropriate attribution, the SGC (a public-private partnership created to place 3D structures of proteins of medical relevance into the public domain) have been able to take the original research articles published in the Collection and create ‘enhanced’ versions of them. As a result each of the research articles is now also available as an ‘interactive’ version, incorporating user manipulable, three-dimensional molecular structures.

Readers of these enhanced articles first need to download a plug-in for their browser but are then able to click on hyperlinked text within the article to ‘fly’ to the relevant position within the molecule, and to interact with it at will (by zooming, rotating, animating, and exploring). The seamless integration of interactive 3D structures into the actual text of the article provides considerable new functionality for readers, and it is hoped it will lead to new insights and discoveries.

A detailed overview explaining how and why the SGC have taken this approach is provided as the first article in the Collection, but this is what two of the SGC researchers had to say about it:

“It’s like directing your own movie to reveal what you want to see. Anyone is now able to look at proteins important for medicine in 3D and move them around as they wish whilst reading about what they are looking at. It’s very intuitive and it should help drug developers in designing new targeted treatments.” (Brian Marsden, SGC)

“At a glance, anyone can now see the proteins for themselves and get all the insight they can by viewing and manipulating the structures in three dimensions whilst reading about what they are seeing. This is far, far better than having to interpret the results of the 500-year-old technology of static images in printed journals.” (Wen Hwa Lee,  SGC)

But don’t take their word for it! Check out the video below which demonstrates some of the interactivity (you should turn on HD and view it in full screen), and then visit any of the articles to try it for yourself (simply click on the “enhanced version” link in the abstract of each article, and install the plug in).

Interactivity Demonstration from brian mossop on Vimeo.

PLoS ONE is excited to launch this Collection, and we will be adding new articles incrementally over time, so check back frequently.

Category: Creative re-use, Functionality | Tagged , | 5 Comments